Monday, February 10, 2014

HGT networks

Introgression is the transfer of genetic material from one species to another via sexual reproduction, and this process has been recognized for a long time. If sex is not involved (such as between distantly related organisms) then we usually refer to it as horizontal gene transfer (HGT), and this has only relatively recently come to the general attention of biologists.

During the 1990s, HGT among prokaryotes began to be taken seriously in phylogenetics (Smith et al. 1992; Syvanen 1994), and more than a decade later also in eukaryotes (see Bock 2010; Boto 2010; Renner & Bellot 2012). However, the question still remains as to when it was first considered within phylogenetics, as opposed to other areas of biology.

It seems that the first report of what was probably HGT in prokaryotes is due to Flu (1927), who of course did not recognize it as such. Indeed, Lederberg & Tatum (1946) also apparently observed HGT, but mistakenly attributed it to sexual recombination (in prokaryotes). This emphasizes just how difficult it can be to identify processes from looking at data patterns.

Further observations were reported by Freeman (1951) and Lederberg et al. (1951). Shortly afterwards, experimental work was published concerning mechanisms for the transfer of genetic material between micro-organisms via what we now call transduction (Zinder & Lederberg 1952; Stocker et al. 1953). The effect of this on phylogenetics was soon considered (Stocker 1955), although no diagrams representing reticulation were presented at this time. The focus was still on elucidating the processes rather than illustrating the phylogenies.

It seems that the first people to actually illustrate HGT among species were Jones & Sneath (1970). In their review of HGT, they not only considered the accumulating evidence for the processes, they explicitly illustrated all of the known cases. These were presented as a series of 18 unrooted phenetic diagrams with known HGT connections linking the bacterial taxa. A single example is shown here.

For eukaryotes, the possibility was early on considered that the asexual transfer of genetic units may be of more general occurrence (Ravin 1955). Indeed, Went (1971) presented a strong case for HGT among plants, based on morphological and anatomical data (ie. phenotypic rather than genotypic evidence). Benveniste & Todaro (1974) then suggested the possibility of exogenously acquired viral genes in mammals. However, it was not really until molecular sequencing became available in the 1980s that biologists really started presenting evidence for gene transfer among eukaryotes (Shilo & Weinberg 1981; Singh et al. 1981; Buslinger et al. 1982; Hyldig-Nielson et al. 1982; Engels 1983).

Most of these suggestions turned out to be spurious, once more evidence accumulated (Smith et al. 1992; Syvanen 1994). However, this did not stop Syvanen (1987) from explicitly considering the effect of HGT on the assessment of evolutionary relationships, apparently being the first to do so. Interestingly, he concluded that "horizontal gene flow would not necessarily preclude a linear molecular clock or change the rate of molecular evolution (assuming the neutral allele theory)."